Q: How do I integrate Heptabase with Zotero?
To integrate Heptabase with your Zotero account:
Go to Tag Database > Add > Connect to Zotero or Settings > Connections > Zotero > Connect.
Log in to your Zotero account and grant the necessary permissions.
Linux troubleshooting: If Zotero shows “Key Saved” but does not return to Heptabase, sign in at app.heptabase.com, then start the connection again from Settings > Connections > Zotero > Connect.
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Q: Why don't I see PDF files after syncing with Zotero?
Heptabase can import attachment files only when they are available for download from your Zotero Web Library. Files synced through WebDAV, linked files stored in Dropbox or another local folder, and local-only files are not downloadable from the Web Library, so Heptabase may import the item metadata without the attachment. If a PDF is missing in Heptabase, work through these checks:
Confirm the PDF is in your Zotero Web Library. If you use a linked file and want it imported into Heptabase, go to Tools > Manage Attachments in Zotero and convert it to a stored file, then confirm that the PDF is downloadable from the Web Library.
Check the file size. Heptabase skips Zotero attachments over 100 MB to keep syncing working. If your PDF exceeds this limit, split it into smaller files in Zotero (for example, by chapter) so each piece is under 100 MB.
Click Re-sync. From the Zotero integration tag group or Settings > Connections > Zotero, trigger a new sync to pull in the latest files.
If the PDF is still missing after these steps, contact support.
Q: How does Zotero sync work?
Heptabase and Zotero perform a one-way sync based on collections. When initiated, Heptabase checks the selected collections in your Zotero Web Library for any new sources or data changes and syncs them accordingly.
Note: Heptabase does not sync with Zotero automatically or on a periodic schedule. To update your data, you must manually trigger the sync via the Tag Database > Zotero Integration tag group or from your Settings.
Q: What Zotero data is imported into Heptabase?
In addition to bibliographic data being converted into source cards, Heptabase imports PDFs, images, videos, notes, and annotations from your selected collections when they are available from the Zotero Web Library. This applies to both standalone items and attachments under a parent item, but not to WebDAV-only files, linked files, or local-only files.
Q: What happens if I click "Disconnect" in Zotero Settings?
When you click Disconnect, you will be prompted to choose whether to permanently delete all data imported from Zotero (including source cards, PDFs, and highlights) or keep it.
If you choose to keep the data, all your information and associated tags will remain intact, allowing you to continue using them seamlessly if you decide to reconnect in the future.
Known limitations in the first version of Zotero integration
You can't see any source cards on the mobile app.
You can't drag source cards onto whiteboards.
You can't see source cards as backlinks.
You can't chat with source cards.